I have noted that using action -> align -> to molecule via the GUI gives
(sometimes radically) different result then running align on the same
structures via command line.

For examples, for PDB structures 4A11 and 3W15, the command
align 4A11,3W15, aligns 1632 atoms and gives an RMSD of 7.538, whereas
action -> align -> to molecule aligns 375 and gives an RMSD of 24.416.
I have also seen such differences on other pairs of structures.

Any explanation of this phenomenon will be most appreciated.

Thanks in advance
Dolev Rahat
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